Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: scaffold3869

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 381

Length: 636
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41


Found at i:107 original size:13 final size:13

Alignment explanation


    Indices: 89--243  Score: 82
    Period size: 13  Copynumber: 11.8  Consensus size: 13

         79 ATTTACTCTT

                        *
         89 AATATATTACTTG
          1 AATATATTACTTA

                         
        102 AATATATTACTTA
          1 AATATATTACTTA

                *        
        115 AATAAATTACTTA
          1 AATATATTACTTA

                *        
        128 AATACATTACTTA
          1 AATATATTACTTA

                      *     
        141 CTAA-A-ATTTCGTTA
          1 --AATATATTAC-TTA

               * *       
        155 AATTTTTTACTTA
          1 AATATATTACTTA

                 *     * 
        168 AATATGTTACTCA
          1 AATATATTACTTA

            *   *    *   
        181 GATACATTAATTA
          1 AATATATTACTTA

                *     **   
        194 CTAAAAT-TTGGTTA
          1 --AATATATTACTTA

               * *       
        208 AATTTTTTACTTA
          1 AATATATTACTTA

                 *       
        221 AATATGTTACTTA
          1 AATATATTACTTA

                *     
        234 AATACATTAC
          1 AATATATTAC

        244 CCGCTATAAA


Statistics
Matches: 106,  Mismatches: 28, Indels: 16
        0.71            0.19        0.11

Matches are distributed among these distances:
  12    5  0.05
  13   85  0.80
  14   12  0.11
  15    4  0.04

ACGTcount: A:0.41, C:0.10, G:0.05, T:0.45


Consensus pattern (13 bp):   
AATATATTACTTA

Found at i:166 original size:53 final size:53

Alignment explanation


    Indices: 108--243  Score: 218
    Period size: 53  Copynumber: 2.6  Consensus size: 53

         98 CTTGAATATA

                       **                                        
        108 TTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT
          1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT

                              * *        *            *          
        161 TTACTTAAATATGTTACTCAGATACATTAATTACTAAAATTTGGTTAAATTTT
          1 TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT

                                          
        214 TTACTTAAATATGTTACTTAAATACATTAC
          1 TTACTTAAATATGTTACTTAAATACATTAC

        244 CCGCTATAAA


Statistics
Matches: 74,  Mismatches: 9, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  53   74  1.00

ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45


Consensus pattern (53 bp):   
TTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTCGTTAAATTTT

Found at i:374 original size:13 final size:13

Alignment explanation


    Indices: 356--407  Score: 70
    Period size: 13  Copynumber: 4.0  Consensus size: 13

        346 TTTTACTCTT

                        *
        356 AATATATTACTTG
          1 AATATATTACTTA

                         
        369 AATATATTACTTA
          1 AATATATTACTTA

                          
        382 AATA-AGTTACTTA
          1 AATATA-TTACTTA

                *        
        395 AATACATTACTTA
          1 AATATATTACTTA

        408 CTAAAATTTC


Statistics
Matches: 36,  Mismatches: 1, Indels: 4
        0.88            0.02        0.10

Matches are distributed among these distances:
  12    1  0.03
  13   34  0.94
  14    1  0.03

ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42


Consensus pattern (13 bp):   
AATATATTACTTA
Done.